sp::over() for point in polygon analysis

Question

I have a shapefile named "ind_adm" and a SpatialPointsDataFrame called "pnts". The "pnts" contains points generated at random, and some of the points overlap with the polygon. See picture below.

Now, I want do do a point in polygon analysis, i.e. I want to find out which points lie inside the gray polygon representing the boundary of India. For this I am using the over() function in the sp library.

pt.in.poly <- sp::over(ind_adm, pnts, fn = mean) #do the join

However, the output I am getting is

    >pt.in.poly
    values
    0 6.019467

I should actually get the index of the points that are "in" the polygon.

Where am I going wrong?

Answer 1

You should not supply a function. You are aggregating the attribute values of your points over the geometry of the polygon, (i.e. the number returned is the mean of the attribute of the points that fall within the polygon). In addition you have your x and y the wrong way round for what you want to do. Should be...

over( pnts , ind_adm , fn = NULL) 

Answer 2

Found this concise and intuitive syntax for over:

   pnts[ind_adm,] 

from this Intro document

Answer 3

You can use point.in.poly fom spatialEco package. It "intersects point and polygon feature classes and adds polygon attributes to points".

library(spatialEco)

new_shape <- point.in.poly(pnts, ind_adm)

Answer 4

You could also use the st_intersection function from the sf package:

Load the library

library(sf)

Create a simple feature geometry (polygon) from your polygon

ind_adm <- st_as_sf(ind_adm)

Create a simple feature geometry (point) from your points of interest

(24047 is the EPSG code for India)

pnts <- st_as_sf(pnts) %>% st_set_crs(., 24047)

Keep only the points inside the polygon

kept_points <- st_intersection(ind_adm, pnts)